FoxWare™, An Advanced Data Analysis Package for Hydroxyl Radical Foot-Printing Higher Order Structural Analysis

The GenNext Phase II SBIR submssion entitled “FoxWare™, an Advanced Data
Analysis Package for Hydroxyl Radical Foot-printing Higher Order Structural Analysis” is
responsive to the ackowledged need for new and improved tools for higher order
structural analysis (HOS) of biopharmaceuticals. Biopharmaceuticals are complex,
heterogeneous mixtures of 3-dimensional biomolecules, whose safety and efficacy is
reliant upon proper HOS. The presence of proteins with improper HOS has been linked
to severe adverse drug reactions (ADR), establishing the need for new and improved
HOS analytics.An emerging HOS analysis technique is hydroxyl radical foot-printing (HRPF).
HRPF involves the irreversible labeling of a protein's exterior by reaction with hydroxyl
radicals with subsequent MS analysis to identify the outer portions of the protein. The
most widely used method for generating OH radicals employs a quick burst of UV light,
and is appropriately called fast photochemical oxidation of proteins (FPOP). Academic
laboratories have demonstrated the utility of FPOP for HOS analysis; however adoption
in pharma has been minuscule at best. Guided by the critiques of scientists at leading
biopharmaceutical companies, we have identified barriers that have limited pharma's
adoption of FPOP HRPF. A substantial barrier is the absence of data processing
tools to facilitate HRPF analysis. Today there are no commercial solutions for FPOP
analysis, despite the demonstrated market need for its HOS analytical power.Today's proteomics data analysis products fail to adequately address specific
work-flow, chemical labeling / artifacts, and comparative study requirements of HRPF
HOS analysis. Researchers are compelled to use a piece-meal approach, arduously
stitching together results from multiple packages and manually manipulating data in
home-brew spreadsheets. As such, data processing represents a significant bottleneck
that greatly complicates and delays progress in HRPF HOS studies. Our FoxWare™
software addresses data processing demands of HRPF HOS analysis. Our proposal
vastly improves HRPF data analysis by replacing laborious and agonizing present-day
practices with an integrated, seamless solution to interpret and amplify the value of
HRPF HOS studies. Upon completion of our envisioned program, FoxWare will make an
indelible mark upon HOS analysis and impart a transformative shift in analytics and
HRPF throughput, addressing the market demands of the biopharmaceutical industry.